The thermal springs along the Middle Fork of the Boise River (MFBR) within the Atlanta lobe of the Idaho batholith discharge in discrete locations that appear to be part of self-organizing flow systems. Infiltrating water flows through Basin and Range fractures to depth where it is heated and ultimately discharged at the intersection of trans-Challis oriented faults along the MFBR. Isotopic compositions of the thermal waters have a linear trend with elevation suggesting that the recharge locations are near each thermal spring and the hydrothermal system is not one large interconnected system, but rather multiple individual hydrothermal systems. Water chemically evolves along the hydrothermal flow paths dissolving feldspars and precipitating secondary minerals. PHREEQC inverse modeling of the chemical evolution based on identified minerals within the system predicts positive volume changes in the pore space within the hydrothermal flow systems can occur. Precipitation of secondary minerals is likely to occur in the cooler, subsidiary, less-efficient fractures of the hydrothermal system. Flow areas calculated using heat flow, exponential decay, and a combination of the two, show that the topographic watershed is inadequate to accommodate the water supporting the thermal springs indicating that water is being captured from outside the watershed. The positive volume changes coupled with the water capture is evidence of positive feedback loops are active within the hydrothermal system providing a mechanism for self-organization to occur in the hydrothermal systems of granite.